First Observation of Cyclotron Radiation from MeV-Scale e

We present an apparatus for detection of cyclotron radiation yielding a frequency-based ß^{±} kinetic energy determination in the 5 keV to 2.1 MeV range, characteristic of nuclear ß decays. The cyclotron frequency of the radiating ß particles in a magnetic field is used to determine the ß energy precisely. Our work establishes the foundation to apply the cyclotron radiation emission spectroscopy (CRES) technique, developed by the Project 8 Collaboration, far beyond the 18-keV tritium endpoint region. We report initial measurements of ß^{-}'s from ^{6}He and ß^{+}'s from ^{19}Ne decays to demonstrate the broadband response of our detection system and assess potential systematic uncertainties for ß spectroscopy over the full (MeV) energy range. To our knowledge, this is the first direct observation of cyclotron radiation from individual highly relativistic ß's in a waveguide. This work establishes the application of CRES to a variety of nuclei, opening its reach to searches for new physics beyond the TeV scale via precision ß-decay measurements.

ß-Nuclear-Recoil Correlation from

We report the first precise measurement of a ß-recoil correlation from a radioactive noble gas (^{6}He) confined via a magneto-optical trap. The measurement is motivated by the search for exotic tensor-type contributions to the charged weak current. Interpreted as tensor currents with right-handed neutrinos, the measurements yield |C_{T}/C_{A}|^{2}≤0.022 (90% confidence limit, C.L.). On the other hand, for left-handed neutrinos the limits are 0.007

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations.

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

Limit on Tensor Currents from

In the standard model, the weak interaction is formulated with a purely vector-axial-vector (V-A) structure. Without restriction on the chirality of the neutrino, the most general limits on tensor currents from nuclear ß decay are dominated by a single measurement of the ß-ν[over ¯] correlation in ^{6}He ß decay dating back over a half century. In the present work, the ß-ν[over ¯]-α correlation in the ß decay of ^{8}Li and subsequent α-particle breakup of the ^{8}Be^{*} daughter was measured. The results are consistent with a purely V-A interaction and in the case of couplings to right-handed neutrinos (C_{T}=-C_{T}^{'}) limits the tensor fraction to |C_{T}/C_{A}|^{2}<0.011 (95.5% C.L.). The measurement confirms the ^{6}He result using a different nuclear system and employing modern ion-trapping techniques subject to different systematic uncertainties.

Single-Electron Detection and Spectroscopy via Relativistic Cyclotron Radiation.

It has been understood since 1897 that accelerating charges must emit electromagnetic radiation. Although first derived in 1904, cyclotron radiation from a single electron orbiting in a magnetic field has never been observed directly. We demonstrate single-electron detection in a novel radio-frequency spectrometer. The relativistic shift in the cyclotron frequency permits a precise electron energy measurement. Precise beta electron spectroscopy from gaseous radiation sources is a key technique in modern efforts to measure the neutrino mass via the tritium decay end point, and this work demonstrates a fundamentally new approach to precision beta spectroscopy for future neutrino mass experiments.

First results from the CARIBU facility: mass measurements on the r-process path.

The Canadian Penning Trap mass spectrometer has made mass measurements of 33 neutron-rich nuclides provided by the new Californium Rare Isotope Breeder Upgrade facility at Argonne National Laboratory. The studied region includes the 132Sn double shell closure and ranges in Z from In to Cs, with Sn isotopes measured out to A=135, and the typical measurement precision is at the 100 ppb level or better. The region encompasses a possible major waiting point of the astrophysical r process, and the impact of the masses on the r process is shown through a series of simulations. These first-ever simulations with direct mass information on this waiting point show significant increases in waiting time at Sn and Sb in comparison with commonly used mass models, demonstrating the inadequacy of existing models for accurate r-process calculations.

ß-delayed neutron spectroscopy using trapped radioactive ions.

A novel technique for ß-delayed neutron spectroscopy has been demonstrated using trapped ions. The neutron-energy spectrum is reconstructed by measuring the time of flight of the nuclear recoil following neutron emission, thereby avoiding all the challenges associated with neutron detection, such as backgrounds from scattered neutrons and γ rays and complicated detector-response functions. (137)I(+) ions delivered from a (252)Cf source were confined in a linear Paul trap surrounded by radiation detectors, and the ß-delayed neutron-energy spectrum and branching ratio were determined by detecting the ß(-) and recoil ions in coincidence. Systematic effects were explored by determining the branching ratio three ways. Improvements to achieve higher detection efficiency, better energy resolution, and a lower neutron-energy threshold are proposed.

Tensor interaction limit derived from the α-ß-ν[over ¯] correlation in trapped 8Li ions.

A measurement of the α-ß-ν[over ¯] angular correlation in the Gamow-Teller decay (8)Li→(8)Be(*)+ν[over ¯]+ß, (8)Be(*)→α+α has been performed using ions confined in a linear Paul trap surrounded by silicon detectors. The energy difference spectrum of the α particles emitted along and opposite the direction of the ß particle is consistent with the standard model prediction and places a limit of 3.1% (95.5% confidence level) on any tensor contribution to the decay. From this result, the amplitude of any tensor component C(T) relative to that of the dominant axial-vector component C(A) of the electroweak interaction is limited to |C(T)/C(A)|<0.18 (95.5% confidence level). This experimental approach is facilitated by several favorable features of the (8)Li ß decay and has different systematic effects than the previous ß-ν[over ¯] correlation results for a pure Gamow-Teller transition obtained from studying (6)He ß decay.

Stimulating effect of growth hormone on type IV collagen production by endothelial cells cultured in normal and high glucose.

Collagen IV accumulation is characteristic of diabetic angiopathy. To test the possible contribution of GH, we studied its effects on collagen IV production by human umbilical vein endothelial cells at 5.5 and 16.7 mmol/l glucose. GH (100 ng/ml) markedly increased collagen IV level in the culture supernatant and in the insoluble extracellular matrix and cell fraction at both glucose concentrations. This stimulating effect of GH was additional to that of high glucose. It was more pronounced on collagen IV than on total protein synthesis. GH increased free latent gelatinase activity slightly at normal and markedly at high glucose. Using GF109203X, a PKC inhibitor, we observed that high glucose, but not GH, activated PKC. These two factors stimulating collagen IV production appear to work through different pathways, favoring an additivity of their effects. This supports the contribution of high plasma GH in diabetic vascular basement membrane thickening.

Proteomic analysis of Plasmodium in the mosquito: progress and pitfalls.

Here we discuss proteomic analyses of whole cell preparations of the mosquito stages of malaria parasite development (i.e. gametocytes, microgamete, ookinete, oocyst and sporozoite) of Plasmodium berghei. We also include critiques of the proteomes of two cell fractions from the purified ookinete, namely the micronemes and cell surface. Whereas we summarise key biological interpretations of the data, we also try to identify key methodological constraints we have met, only some of which we were able to resolve. Recognising the need to translate the potential of current genome sequencing into functional understanding, we report our efforts to develop more powerful combinations of methods for the in silico prediction of protein function and location. We have applied this analysis to the proteome of the male gamete, a cell whose very simple structural organisation facilitated interpretation of data. Some of the in silico predictions made have now been supported by ongoing protein tagging and genetic knockout studies. We hope this discussion may assist future studies.

Acute HIV infections among men with genital ulcer disease in South Africa.

We investigated acute human immunodeficiency virus (HIV) infection among men enrolled in a genital ulcer treatment trial in South Africa. HIV-negative participants were tested at baseline by HIV RNA polymerase chain reaction and followed up after 1 month to measure HIV seroconversion. There were 228 HIV-negative men at baseline; 10 were positive for HIV RNA, and 8 seroconverted to HIV at day 28. The prevalence of acute HIV among HIV-negative men at baseline was 18 (7.9%) of 228 men (95% confidence interval [CI], 4.4-11.4) and 18 (2.9%) of 615 men (95% CI, 1.6-4.3) in the overall study population. These data highlight the importance of genital ulcer patients in HIV transmission. Trial Registration. ClinicalTrials.gov identifier: NCT00164424 .

Lysinoalanine: presence in foods and food ingredients.

Lysinoalanine, N6-(DL-2-amino-2-carboxyethyl)-L-lysine, an unusual amino acid implicated as a renal toxic factor in rats, has been found in proteins of home-cooked and commercial foods and ingredients. Although it has been reported to occur in both edible and nonfood proteins only after alkali treatment, it has now been identified in food proteins that had not been subjected to alkali. Lysinoalanine is generated in a variety of proteins when heated under nonalkaline conditions.

Reproducibility and specificity concerns associated with nucleic acid amplification tests for detecting Chlamydia trachomatis.

Commercial nucleic acid amplification tests (NAATs) have become one of the most frequently used tests for detecting Chalmydia trachomatis. However, published studies have raised important concerns regarding the NAAT evaluation process in general and their reproducibility and clinical specificity in particular. This is because for many infectious diseases including chlamydia, a true gold standard simply does not exist and, as a result, estimation of test performance parameters in the absence of a gold standard is a difficult and challenging task. In this manuscript, we will attempt to address some issues pertaining to the evaluation of NAATs including NAAT reproducibility, test validity, and the manner in which positive NAAT results are confirmed. Finally, we will discuss some of the potential clinical and public health implications of testing by NAATs.

Autoimmune disease and molecular mimicry: an hypothesis.

Helper T lymphocytes are normally only stimulated to initiate an immune reaction through the recognition of peptides bound to class II major histocompatibility complex (MHC) molecules. Class II MHC molecules are constitutively expressed on antigen-presenting cells which play a critical role in the initiation of immune responses. In disease states, however, other cells often express class II MHC molecules inappropriately. This article suggests an hypothesis for the pathogenesis of autoimmune diseases based on molecular mimicry. The mimicry described is between microbial or viral peptides presented by antigen-presenting cells and self peptides presented inappropriately on a target tissue. This leads to helper T cells, stimulated by peptides derived from infectious organisms, initiating an autoimmune attack on the target tissue.

EMAAS: an extensible grid-based rich internet application for microarray data analysis and management.

BACKGROUND: Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. RESULTS: EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. CONCLUSION: EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume.

Structure prediction. How good are we?

Recent successes show that, in certain circumstances, protein secondary structures can be predicted with high accuracy. How far are we from being able to predict the complete structure of a protein from its sequence?

Aspirin inhibits the formation of pentosidine, a cross-linking advanced glycation end product, in collagen.

Aspirin showed an inhibitory effect on the formation of pentosidine, a cross-linking advanced glycation endproduct, in collagen incubated with glucose in vitro. IC(50) was evaluated at 10mmol/l. Aspirin might act by metallic ion chelating (as did EDTA and DTPA) and by oxygen radical scavenging. Since aspirin was reported to inhibit retinopathy in diabetic dogs, it could act partly by inhibiting advanced glycation endproduct accumulation in long-lived proteins like collagens.

Predictive docking of protein-protein and protein-DNA complexes.

Recent developments in algorithms to predict the docking of two proteins have considered both the initial rigid-body global search and subsequent screening and refinement. The result of two blind trials of protein docking are encouraging--for complexes that are not too large and do not undergo sizeable conformational change upon association, the algorithms are now able to suggest reasonably accurate models.

Progress in protein structure prediction: assessment of CASP3.

The third comparative assessment of techniques of protein structure prediction (CASP3) was held during 1998. This is a blind trial in which structures are predicted prior to having knowledge of the coordinates, which are then revealed to enable the assessment. Three sections at the meeting evaluated different methodologies - comparative modelling, fold recognition and ab initio methods. For some, but not all of the target coordinates, high quality models were submitted in each of these sections. There have been improvements in prediction techniques since CASP2 in 1996, most notably for ab initio methods.